Name Nicholas Harris

Exploring Protein Structure Worksheet

Biology 205, Fall 2014, 6 points total
Please note: to draw arrows with the most recent version of MS word, select the insert tab, then
shapes, then lines as shown below.

1) (0.5 pt) Paste amino acid 1 below in the CPK coloration mode (carbon-gray, hydrogenwhite, nitrogen-blue, oxygenred, sulfur-yellow; recall that CPK is a coloration mode and is
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not the same as space filled).

A) Use the table of amino acid structures to identify amino acid 1.

The amino acid structure is Serine
B) Use arrows to indicate the amino, carboxyl, and side chain groups on the amino acid.
Red= Side Chain, Blue= Amino, Black=Carboxyl
C) Identify whether or not the side chain is hydrophobic or hydrophilic.
The Side Chain is hydrophobic

2) (0.5 pt) Paste in amino acid 2 in the CPK coloration mode.

A) Use the table of amino acid structures to identify amino acid 2.
Tyrosine
B) Use arrows to indicate the amino, carboxyl, and side chain groups on the amino acid.
Red= Side Chain Group, Blue=Carboxyl, Black=Amino group
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C) Identify whether or not the side chain is hydrophobic or hydrophilic.

It shows both properties but is slightly more hydrophilic because of the OH

3) (0.5 pt) Paste in the alpha helix backbone in the CPK coloration mode showing the
hydrogen bonds that stabilize the alpha helix. What is the length of one turn of this alpha
helix?
.464 nm

4) (0.5 pt) Paste in the beta sheet backbone in the CPK coloration mode showing the
hydrogen bonds that stabilize the beta sheet. What is the distance between the two
parallel strands of the beta sheet?
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The distance is .501nm.

5) (0.5 pt) Paste in the beta sheet showing side chains. Identify the peptide bond
between tyrosine and serine with an arrow.
See Above

6) (0.5 pt) Paste in a ball and stick version of Ras, showing the backbone only. Identify
possible alpha helices and a beta sheet with arrows.
Top image shows the beta sheets and the bottom image the alpha helices

7) (0.5 pt) Paste the cartoon version of Ras, in the same orientation as in question 6. Did you
correctly identify alpha helices and a beta-sheet?
Yes wee did correctly identify them

8) (0.5 pt) Paste in a ball and stick model of Ras with the polar amino acids colored in green
and the non-polar amino acids colored in yellow. Are non-polar or polar amino acids more
likely to be buried in the interior? Briefly explain why.
The non polar amino acids are more likely to be buried in the interior because they are
hydrophobic.

9) (1 pt) Paste in Ras as space-filled with green polar side chains, yellow non-polar side
chains and white protein backbone without GTP. Then, paste in Ras with GTP.
A) How tightly does GTP fit into the GTP-binding pocket of Ras?
It fits in very tightly but it is still partially exposed
B) Identify four amino acids that are in the GTP-binding pocket. Note that an amino acid
name code appears in a small box when the cursor hovers over each amino acid.
Glycine, Aspartic Acid, Lysine, Tyrosine
C) Are these amino acids contiguous (i.e. adjacent in the primary structure/amino acid
sequence) with each other on the polypeptide chain? Note that a number indicating the
position of the amino acid on the polypeptide chain also appears as above.
They are continuous with each other in the polypeptide chain.

10) (1 pt) Paste in an image of hemoglobin with measurements.

A) What is the approximate diameter of a hemoglobin tetramer? Make 3-4 measurements
and take the average to calculate the diameter: __5.686nm_____________

B) What is the mean center to center distance between hemoglobin tetramers in a red
blood cell? To estimate the spacing of hemoglobin tetramers within the cell, the following
formula can be employed: d = (V/N)0.33. (d = mean center to center distance of
hemoglobin tetramers; V = volume of a red blood cell, 30 m3; N = number of
hemoglobin tetramers per cell, 0.75 x108).
Please note that you will first want to convert 30 m3 to nm3 because your measurements
of the diameter of the hemoglobin tetramer are in nm. A good starting point is to recall
that 1 m = 103 nm.
30 m 3 = __3x10^10____ nm3
Mean center to center distance between tetramers: ____7.222nm_______
B) How tightly packed are hemoglobin tetramers in a red blood cell? Use the average
diameter of the tetramer from A and the center to center spacing between tetramers
from B to estimate the average distance between two hemoglobin molecules inside a
red blood cell. Drawing a diagram may help.
The estimate average distance between two hemoglobin would be 153637nm